Preheat oven to 375°F. In large skillet, heat oil over medium heat. Add squash and zucchini. Cook, stirring, until vegetables are browned, about 8 minutes. Cool 5 minutes.
In large bowl, combine squash, zucchini, ricotta, 1 cup provolone, Parmesan, eggs, parsley, salt, and pepper. Transfer cheese mixture to a large resealable storage bag. Push mixture toward one corner and twist bag closed. Make a 3/4 inch cut in a corner of bag, and squeeze filling into each pasta tube.
In bowl, combine marinara sauce and water. Spread 2/3 cup each into two 2-quart baking dishes. Divide manicotti between baking dishes, arranging in a single layer. Top with remaining marinara sauce.
Cover 1 pan with foil and bake 45 minutes. Remove foil and sprinkle with 1/4 cup provolone cheese. Bake at 375°F for 10 minutes, or until cheese melts.
Cover remaining dish tightly with a double layer of plastic wrap and freeze.
Thaw in refrigerator overnight. Remove plastic wrap, cover with foil, and follow baking directions in step 4.
